def coloumb_configured_interface(iface, random=True,
translations=None,
rotations=None,
samples=10, lowest=5, ecut=None):
"""
Creates Ligand Slab interfaces of user specified translations
and rotations away from the initial guess of binding site
configuration, returns lowest energy structure according to
Coulomb model
Args:
Interface: Interface object: initial interface object
random: True for using Gaussian sampled random numbers for
rotations and translations
translations: list of [x,y,z] translations to be performed
rotation: list of [a,b,c] rotations to be performed w.r.t
Ligand axis
samples: number of interfaces to create
lowest: number of structures to return according to order of
minimum energies
Returns:
list of lowest energy interface objects
"""
ifaces = []
transform = []
for i in range(samples):
if random:
x = np.random.normal() # shift along x direction
y = np.random.normal() # shift along y direction
z = np.random.normal() # shift aling z direction
a = SymmOp.from_axis_angle_and_translation(axis=[1, 0, 0], \
angle=np.random.normal(0, 180))
b = SymmOp.from_axis_angle_and_translation(axis=[0, 1, 0], \
angle=np.random.normal(0, 180))
c = SymmOp.from_axis_angle_and_translation(axis=[0, 0, 1], \
angle=np.random.normal(0, 180))
ligand = iface.ligand
ligand.apply_operation(a)
ligand.apply_operation(b)
ligand.apply_operation(c)
# check if created interface maintains the ligand adsorbed
# over the surface
for j in iface.top_atoms:
if not iface.cart_coords[j][2] + iface.displacement > \
min(ligand.cart_coords[:, 2]):
transform.append(True)
if all(transform):
iface = Interface(iface.strt, hkl=iface.hkl,
min_thick=iface.min_thick,
min_vac=iface.min_vac,
supercell=iface.supercell,
surface_coverage=iface.surface_coverage,
ligand=iface.ligand, displacement=z,
adatom_on_lig=iface.adatom_on_lig,
adsorb_on_species=iface.adsorb_on_species,
primitive=False, from_ase=True,
x_shift=x, y_shift=y)
iface.create_interface()
energy = iface.calc_energy()
iface.sort()
if energy < ecut:
ifaces.append((energy, iface))
# ifaces.zip(energy, iface)
return ifaces
def coloumb_configured_interface(iface, random=True,
translations= None,
rotations=None,
samples=10, lowest=5, ecut=None):
"""
Creates Ligand Slab interfaces of user specified translations
and rotations away from the initial guess of binding site
configuration, returns lowest energy structure according to
Coulomb model
Args:
Interface: Interface object: initial interface object
random: True for using Gaussian sampled random numbers for
rotations and translations
translations: list of [x,y,z] translations to be performed
rotation: list of [a,b,c] rotations to be performed w.r.t
Ligand axis
samples: number of interfaces to create
lowest: number of structures to return according to order of
minimum energies
Returns:
list of lowest energy interface objects
"""
ifaces= []
transform= []
for i in range(samples):
if random:
x = np.random.normal() # shift along x direction
y = np.random.normal() # shift along y direction
z = np.random.normal() # shift aling z direction
a= SymmOp.from_axis_angle_and_translation(axis=[1,0,0],\
angle=np.random.normal(0,180))
b= SymmOp.from_axis_angle_and_translation(axis=[0,1,0],\
angle=np.random.normal(0,180))
c= SymmOp.from_axis_angle_and_translation(axis=[0,0,1],\
angle=np.random.normal(0,180))
ligand=iface.ligand
ligand.apply_operation(a)
ligand.apply_operation(b)
ligand.apply_operation(c)
# check if created interface maintains the ligand adsorbed
# over the surface
for j in iface.top_atoms:
if not iface.cart_coords[j][2] + iface.displacement > \
min(ligand.cart_coords[:,2]):
transform.append(True)
if all(transform):
iface= Interface(iface.strt, hkl=iface.hkl,
min_thick=iface.min_thick,
min_vac=iface.min_vac,
supercell=iface.supercell,
surface_coverage=iface.surface_coverage,
ligand=iface.ligand, displacement=z,
adatom_on_lig=iface.adatom_on_lig,
adsorb_on_species=iface.adsorb_on_species,
primitive= False, from_ase=True,
x_shift=x, y_shift=y)
iface.create_interface()
energy= iface.calc_energy()
iface.sort()
if energy<ecut:
ifaces.append((energy,iface))
# ifaces.zip(energy, iface)
return ifaces
# adsorb_on_species atom
# on the slab
# in Angstrom
displacement = 3.0
# here we create the adsorbate slab Interface
iface = Interface(strt, hkl=hkl, min_thick=min_thick,
min_vac=min_vac, supercell=supercell,
surface_coverage=surface_coverage,
ligand=hydrazine, displacement=displacement,
adatom_on_lig=adatom_on_lig,
adsorb_on_species=adsorb_on_species,
primitive=False, from_ase=True)
iface.create_interface()
iface.sort()
energy = iface.calc_energy()
iface.to('poscar', 'POSCAR_interface.vasp')
interfaces = coloumb_configured_interface(iface, random=True,
translations=None,
rotations=None,
samples=20, lowest=5,
ecut=energy)
for i, iface in enumerate(interfaces):
print("Coloumb Energy")
print(i, iface[0])
iface[1].to('poscar', 'POSCAR_interface' + str(iface[0]) + '.vasp')
iface_slab = iface[1].slab
iface_slab.sort()
# set selective dynamics flags as required
true_site = [1, 1, 1]
false_site = [0, 0, 0]
#adsorb_on_species atom
#on the slab
#in Angstrom
displacement = 3.0
#here we create the adsorbate slab Interface
iface = Interface(strt, hkl=hkl, min_thick=min_thick,
min_vac=min_vac, supercell=supercell,
surface_coverage=surface_coverage,
ligand=hydrazine, displacement=displacement,
adatom_on_lig=adatom_on_lig,
adsorb_on_species= adsorb_on_species,
primitive= False, from_ase=True)
iface.create_interface()
iface.sort()
energy=iface.calc_energy()
iface.to('poscar','POSCAR_interface.vasp')
interfaces= coloumb_configured_interface(iface, random=True,
translations= None,
rotations=None,
samples=20, lowest=5,
ecut=energy)
for i, iface in enumerate(interfaces):
print ("Coloumb Energy")
print (i, iface[0])
iface[1].to('poscar', 'POSCAR_interface'+str(iface[0])+'.vasp')
iface_slab = iface[1].slab
iface_slab.sort()
#set selective dynamics flags as required
true_site= [1, 1, 1]
false_site= [0, 0, 0]
